v0.28.0

• Normalize command code changed to be more idiomatic python and more idiomatic numpy usage

• Tests added for normalize command

• Fixes some problems with region calculations in normalize command:

  • mergeRegions created 0-length overlaps. if two regions are next to
    each other they get merged, but they don't overlap. A zero-length
    overlap is created, which can cause a problem later when trying to
    get reads from the bigwig file.

  • region_overlap entries might have the wrong end.

    (line 80) region_overlapped.append([currChromo, currStart, pastEnd])

    is incorrect if currEnd is < pastEnd. Changed to

    region_overlapped.append([currChromo, currStart, min(currEnd, pastEnd)])

  • excludeOverlapRegion didn't fully separate region overlap cases.
    "overlap regions end inside the target region" and "overlap regions
    start inside the target region" can share some overlaps when one
    starts and ends in the same region. This Fourth case is now
    handled separately.

  • in excludeOverlapRegion calculating non-overlapping regions had some subtle
    bugs.